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Series GSE197838 Query DataSets for GSE197838
Status Public on Sep 30, 2023
Title Affymetrix SNP array data for acute lymphoblastic leukemia samples
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary In precursor B-cell acute lymphoblastic leukemia (ALL), whole chromosome uniparental isodisomy (wUPD) occurs almost uniquely in the high hyperdiploid (51-67 chromosomes) (HH) subtype. Comparison of 26 HH with wUPD with 31 with noUPD, showed a higher modal number of chromosomes and gains of 5+ in wUPD. Mutations in genes within epigenetic pathways with upregulation of genes involved in cellular response to stress and stimuli, and mutations in RAS/RTK pathways and upregulation of genes in RNA Polymerase III pathway were seen in wUPD and noUPD respectively. Though overall outcomes were similar in patient with and without wUPD, those with noUPD were more likely to have residual disease after treatment. Differential gene expression between the two groups showed upregulation of genes involved in thiopurine drug resistance in wUPD. Genome-wide differences between HH ALL with and without UPD identified plausible biological explanations for the heterogeneity in therapeutic response in HH ALL.
 
Overall design Copy number analysis of Affymetrix CytoscanHD SNP arrays was performed for 56 pediatric High hyperdiploid Acute Lymphoblastic Leukemia samples.
 
Contributor(s) Parihar M, Saha V
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Submission date Mar 03, 2022
Last update date Sep 30, 2023
Contact name Mayur Parihar
E-mail(s) mayur.parihar@ttcrc.tmckolkata.org
Organization name Tata Medical Center
Department Pathology
Lab Cytogenetics and Genomics
Street address 14 Major Arterial Road (E-W)
City Kolkata
State/province West Bengal
ZIP/Postal code 700160
Country India
 
Platforms (1)
GPL16131 [CytoScanHD_Array] Affymetrix CytoScan HD Array
Samples (56)
GSM5931184 2.7yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_1
GSM5931185 2.08yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_2
GSM5931186 2.8yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_3
Relations
BioProject PRJNA812429

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE197838_RAW.tar 6.6 Gb (http)(custom) TAR (of CEL, CYCHP)
Processed data provided as supplementary file

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